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Install Packages

#install packages
install.packages("BiocManager")
Error in install.packages : Updating loaded packages
install.packages("forcats")
Installing package into ‘/home/mouse/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/forcats_1.0.0.tar.gz'
Content type 'application/x-gzip' length 294183 bytes (287 KB)
==================================================
downloaded 287 KB

* installing *source* package ‘forcats’ ...
** package ‘forcats’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (forcats)

The downloaded source packages are in
    ‘/tmp/RtmpVpfP8o/downloaded_packages’
install.packages("stringr")
Installing package into ‘/home/mouse/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/stringr_1.5.0.tar.gz'
Content type 'application/x-gzip' length 175699 bytes (171 KB)
==================================================
downloaded 171 KB

* installing *source* package ‘stringr’ ...
** package ‘stringr’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (stringr)

The downloaded source packages are in
    ‘/tmp/RtmpVpfP8o/downloaded_packages’
install.packages("BiocManager")
Installing package into ‘/home/mouse/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/BiocManager_1.30.20.tar.gz'
Content type 'application/x-gzip' length 265248 bytes (259 KB)
==================================================
downloaded 259 KB

* installing *source* package ‘BiocManager’ ...
** package ‘BiocManager’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BiocManager)

The downloaded source packages are in
    ‘/tmp/RtmpVpfP8o/downloaded_packages’
install.packages("ggplot2")
Installing package into ‘/home/mouse/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/ggplot2_3.4.1.tar.gz'
Content type 'application/x-gzip' length 3150856 bytes (3.0 MB)
==================================================
downloaded 3.0 MB

* installing *source* package ‘ggplot2’ ...
** package ‘ggplot2’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ggplot2)

The downloaded source packages are in
    ‘/tmp/RtmpVpfP8o/downloaded_packages’
install.packages("ggrepel")
Installing package into ‘/home/mouse/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/ggrepel_0.9.3.tar.gz'
Content type 'application/x-gzip' length 136189 bytes (132 KB)
==================================================
downloaded 132 KB

* installing *source* package ‘ggrepel’ ...
** package ‘ggrepel’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c repel_boxes.cpp -o repel_boxes.o
g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o ggrepel.so RcppExports.o repel_boxes.o -L/usr/lib/R/lib -lR
installing to /home/mouse/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-ggrepel/00new/ggrepel/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ggrepel)

The downloaded source packages are in
    ‘/tmp/RtmpVpfP8o/downloaded_packages’
install.packages("readr")
Installing package into ‘/home/mouse/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/readr_2.1.4.tar.gz'
Content type 'application/x-gzip' length 298083 bytes (291 KB)
==================================================
downloaded 291 KB

* installing *source* package ‘readr’ ...
** package ‘readr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Collector.cpp -o Collector.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c CollectorGuess.cpp -o CollectorGuess.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Iconv.cpp -o Iconv.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c LocaleInfo.cpp -o LocaleInfo.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Reader.cpp -o Reader.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Source.cpp -o Source.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Tokenizer.cpp -o Tokenizer.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c TokenizerDelim.cpp -o TokenizerDelim.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c TokenizerFwf.cpp -o TokenizerFwf.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c TokenizerWs.cpp -o TokenizerWs.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c connection.cpp -o connection.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c cpp11.cpp -o cpp11.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c datetime.cpp -o datetime.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c grisu3.c -o grisu3.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c init.c -o init.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c parse.cpp -o parse.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c read.cpp -o read.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c type_convert.cpp -o type_convert.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c write.cpp -o write.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG  -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include' -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/tzdb/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c write_delim.cpp -o write_delim.o
g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o readr.so Collector.o CollectorGuess.o Iconv.o LocaleInfo.o Reader.o Source.o Tokenizer.o TokenizerDelim.o TokenizerFwf.o TokenizerWs.o connection.o cpp11.o datetime.o grisu3.o init.o parse.o read.o type_convert.o write.o write_delim.o -L/usr/lib/R/lib -lR
installing to /home/mouse/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-readr/00new/readr/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (readr)

The downloaded source packages are in
    ‘/tmp/RtmpVpfP8o/downloaded_packages’
install.packages("tidyr")
Installing package into ‘/home/mouse/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/tidyr_1.3.0.tar.gz'
Content type 'application/x-gzip' length 823546 bytes (804 KB)
==================================================
downloaded 804 KB

* installing *source* package ‘tidyr’ ...
** package ‘tidyr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c cpp11.cpp -o cpp11.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c melt.cpp -o melt.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG  -I'/home/mouse/R/x86_64-pc-linux-gnu-library/4.2/cpp11/include'    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c simplifyPieces.cpp -o simplifyPieces.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o tidyr.so cpp11.o melt.o simplifyPieces.o -L/usr/lib/R/lib -lR
installing to /home/mouse/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-tidyr/00new/tidyr/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (tidyr)

The downloaded source packages are in
    ‘/tmp/RtmpVpfP8o/downloaded_packages’
install.packages("survminer")
Installing package into ‘/home/mouse/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/survminer_0.4.9.tar.gz'
Content type 'application/x-gzip' length 3599577 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

* installing *source* package ‘survminer’ ...
** package ‘survminer’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (survminer)

The downloaded source packages are in
    ‘/tmp/RtmpVpfP8o/downloaded_packages’
BiocManager::install("GEOquery")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.2 Patched (2022-11-10 r83330)
Warning: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'GEOquery'Installation paths not writeable, unable to update packages
  path: /usr/lib/R/library
  packages:
    boot, foreign, Matrix, spatial
BiocManager::install("limma")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.2 Patched (2022-11-10 r83330)
Warning: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'limma'Installation paths not writeable, unable to update packages
  path: /usr/lib/R/library
  packages:
    boot, foreign, Matrix, spatial
BiocManager::install("pheatmap")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.2 Patched (2022-11-10 r83330)
Warning: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'pheatmap'Installation paths not writeable, unable to update packages
  path: /usr/lib/R/library
  packages:
    boot, foreign, Matrix, spatial
BiocManager::install("org.Hs.eg.db")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.2 Patched (2022-11-10 r83330)
Warning: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'org.Hs.eg.db'Installation paths not writeable, unable to update packages
  path: /usr/lib/R/library
  packages:
    boot, foreign, Matrix, spatial

Importing the data. The function to download a GEO data-set is getGEO from GEOquery package.

library(GEOquery)
Registered S3 method overwritten by 'data.table':
  method           from
  print.data.table     
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
#Passive smoker dataset
my_idPS <- "GSE18044"
#Active Smoker Data set
my_idAS <- "GSE27272"

gsePS <- getGEO(my_idPS)
Found 1 file(s)
GSE18044_series_matrix.txt.gz
gseAS <- getGEO(my_idAS)
Found 1 file(s)
GSE27272_series_matrix.txt.gz

Some data-sets on GEO may be derived from different micro-array platforms. Therefore the object gse is a list of different data-sets. You can find out how many were used by checking the length of the gse object. Usually there will only be one platform and the dataset we want to analyse will be the first object in the list (gse[[1]]). If more than one dataset is present, you can analyse the other dataset by changing the number inside the [[…]] ## e.g. gse <- galse[[2]] Check how many platforms used

print(length(gsePS))
[1] 1
print(length(gseAS))
[1] 1
gsePS <- gsePS[[1]]
gsePS
ExpressionSet (storageMode: lockedEnvironment)
assayData: 11155 features, 76 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: GSM451162 GSM451163 ... GSM451237 (76 total)
  varLabels: title geo_accession ... status:ch1 (46 total)
  varMetadata: labelDescription
featureData
  featureNames: ILMN_1343291 ILMN_1343292 ... ILMN_2038778 (11155 total)
  fvarLabels: ID Species ... GB_ACC (26 total)
  fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
  pubMedIds: 20092892 
Annotation: GPL6104 
gseAS <- gseAS[[1]]

Check the normalisation and scales used. For visualization and statistical analysis, we will inspect the data to discover what scale the data are presented in. The methods we will use assume the data are on a log2 scale; typically in the range of 0 to 16. The exprs function can retrieve the expression values as a data frame; with one column per-sample and one row per-gene.

#Passive Smoking Dataset
pData(gsePS) ## print the sample information
fData(gsePS) ## print the gene annotation
exprs(gsePS) ## print the expression data
             GSM451162 GSM451163 GSM451164 GSM451165 GSM451166 GSM451167 GSM451168 GSM451169 GSM451170 GSM451171 GSM451172 GSM451173
ILMN_1343291    149.38    161.57    155.86    155.13    130.20    153.16    170.44    205.75    145.86    153.64    181.06    116.34
ILMN_1343292    149.38    161.57    155.86    155.13    130.20    153.16    170.44    205.75    145.86    153.64    181.06    116.34
ILMN_1343293    259.05    329.22    301.73    247.79    270.24    256.82    253.69    265.28    273.89    296.67    283.68    289.36
ILMN_1343294     69.95     96.98     81.77     67.75     77.58     69.91     70.34     69.59     73.38     73.37     82.37     84.03
ILMN_1651228    248.58    159.55    140.13    197.94    222.67    202.40    207.33    217.45    388.62    148.81    206.83    225.91
ILMN_1651229    960.18    915.18    982.76   1005.17    866.05    862.65    815.36   1006.45    801.85    856.01   1052.66    965.98
ILMN_1651237    185.23    200.89    227.25    181.25    197.69    224.51    254.41    204.17    188.95    228.36    236.14    225.36
ILMN_1651254    154.86    114.90    135.19    124.11    146.09    121.58    175.21    150.20    154.52    153.35    193.97    134.58
ILMN_1651261    248.58    159.55    140.13    197.94    222.67    202.40    207.33    217.17    388.62    148.81    206.83    225.91
ILMN_1651262    291.69    264.66    216.53    357.54    241.07    215.51    238.92    243.78    322.73    259.96    317.24    236.14
ILMN_1651268    117.79     82.40     70.78     83.01    104.68     79.18     73.33     80.09     85.31     98.57    104.95     67.06
ILMN_1651278     75.19     67.51     71.18     67.60     85.05     74.53     74.08     76.30     88.51     62.36     71.45    104.04
ILMN_1651282   1523.99   1370.75   1335.80   1648.18   1622.62   1805.98   1427.94   1414.23   1530.31   1356.39   1712.23   2297.66
             GSM451174 GSM451175 GSM451176 GSM451177 GSM451178 GSM451179 GSM451180 GSM451181 GSM451182 GSM451183 GSM451184 GSM451185
ILMN_1343291    135.82    140.63    122.72    140.27    117.25    126.55    124.66    159.02    109.61    116.45    148.11    120.12
ILMN_1343292    135.82    140.63    122.72    140.27    117.25    126.55    124.66    159.02    109.61    116.45    148.11    120.12
ILMN_1343293    287.91    280.99    268.45    269.44    244.39    286.78    294.58    250.08    190.45    208.14    272.25    229.67
ILMN_1343294     76.84     70.19     80.26     72.89     74.00     73.37     65.88     67.17     65.31     68.03     69.50     70.74
ILMN_1651228    199.70    207.73    363.54     68.43    145.88    251.22    121.05    127.00    354.33    359.75    224.58   1542.59
ILMN_1651229    771.40    992.70    770.97   1036.26    937.96    944.27    991.32    940.97    965.40    863.47    863.47    778.51
ILMN_1651237    204.28    190.76    230.32    223.87    227.74    197.19    208.40    191.11    215.24    184.17    223.37    144.75
ILMN_1651254    150.85    147.90    123.81    154.14    165.56    146.48    189.02    181.22    138.54    141.18    143.26    132.81
ILMN_1651261    199.70    207.73    363.54     68.43    145.88    251.22    121.05    127.00    354.33    359.75    224.58   1542.59
ILMN_1651262    242.66    235.72    212.60    249.40    284.87    231.42    219.94    237.46    226.53    336.14    277.44    256.00
ILMN_1651268     82.46     91.38     69.36     90.63     89.68     70.87     92.52     85.28     64.79     77.59     65.14     79.42
ILMN_1651278     67.96    111.17    153.81     72.99     78.09     92.07     77.04     90.11     95.19    125.62     87.57    149.12
ILMN_1651282   2487.78   1693.46   1606.46   2421.18   2157.73   2091.75   2232.53   1735.75   2029.32   1800.43   1918.57   1599.61
             GSM451186 GSM451187 GSM451188 GSM451189 GSM451190 GSM451191 GSM451192 GSM451193 GSM451194 GSM451195 GSM451196 GSM451197
ILMN_1343291    156.25    130.79    139.19    144.70    137.22    151.76    147.32    153.94    139.27    159.41    108.50    151.16
ILMN_1343292    156.25    130.79    139.19    144.70    137.22    151.76    147.32    153.94    139.27    159.41    108.50    151.16
ILMN_1343293    304.11    307.44    267.39    218.56    221.34    219.72    200.32    251.69    338.29    276.62    281.33    292.23
ILMN_1343294     94.36     69.99     76.94     64.30     69.60     76.86     68.53     66.73     62.16     73.80     61.24     59.93
ILMN_1651228   1195.60    130.15    173.01    350.58    287.11    347.81    371.58    180.17    314.99    232.66    455.84    449.19
ILMN_1651229    779.19    917.32    974.50    873.58    956.78    867.57    869.03   1165.13   1258.45   1274.96    986.63   1092.54
ILMN_1651237    251.59    171.58    187.96    106.05    197.40    189.40    175.45    195.37    191.11    172.60    183.90    173.19
ILMN_1651254    155.63    157.59    144.40    160.57    151.16    161.28    173.93    153.81    195.43    167.58    129.82    152.75
ILMN_1651261   1195.60    130.15    173.01    350.58    287.11    347.81    371.58    180.17    314.99    232.66    455.84    449.19
ILMN_1651262    349.59    263.48    209.32    273.57    243.55    324.79    347.75    337.86    317.51    279.44    203.24    232.98
ILMN_1651268     72.61    101.26     76.68     78.39     79.23     70.24    103.81     71.88     61.26     71.64     94.84     70.55
ILMN_1651278     75.06     71.40     64.27    190.19     99.86     87.91    107.76     72.39     84.04    109.42    171.98    110.81
ILMN_1651282   1728.11   1999.94   1834.85   1984.98   1977.11   1400.14   1387.58   1837.92   2128.59   2075.09   1604.80   1855.47
             GSM451198 GSM451199 GSM451200 GSM451201 GSM451202 GSM451203 GSM451204 GSM451205 GSM451206 GSM451207 GSM451208 GSM451209
ILMN_1343291    147.38    161.12    166.02    168.01    160.30    139.11    132.07    137.01    151.44    164.30    149.34    157.78
ILMN_1343292    147.38    161.12    166.02    168.01    160.30    139.11    132.09    137.01    151.44    164.30    149.34    157.78
ILMN_1343293    296.03    270.73    283.56    278.87    333.26    296.95    292.98    279.34    260.53    287.62    279.80    313.08
ILMN_1343294     64.49     63.07     66.50     61.48    107.64     67.25     69.91     65.36     68.40     72.00     63.73     72.41
ILMN_1651228    225.16    272.52    230.20    495.25    201.48    222.82    146.20    124.65    121.05    127.70    187.07    218.86
ILMN_1651229   1215.38   1272.01   1087.24   1266.36    753.72    930.65    860.29    768.61    925.23    943.73    851.13    900.15
ILMN_1651237    168.08    197.10    202.14    197.00    370.68    207.11    228.77    235.38    210.31    204.11    201.96    249.48
ILMN_1651254    167.86    191.29    148.40    165.71    135.94    132.41    134.63    135.28    194.71    174.99    150.75    175.39
ILMN_1651261    225.16    272.52    230.20    495.25    201.48    222.82    146.20    124.65    121.05    127.70    187.07    218.86
ILMN_1651262    235.83    258.79    276.86    269.67    252.64    225.04    280.99    192.83    197.66    254.87    194.78    234.34
ILMN_1651268     78.00     76.42     86.98     76.58     89.30     80.25     79.68     97.89     93.44     92.36    119.44     76.82
ILMN_1651278    118.11    107.63     98.88    148.79     76.67     89.43    104.57     72.99     76.64    103.82     72.09     85.16
ILMN_1651282   1809.03   2052.69   1974.94   1984.98   2173.90   1882.37   1900.94   1895.74   1518.89   1786.33   2086.73   2349.43
             GSM451210 GSM451211 GSM451212 GSM451213 GSM451214 GSM451215 GSM451216 GSM451217 GSM451218 GSM451219 GSM451220 GSM451221
ILMN_1343291    146.32    142.71    161.47    161.04    126.72    123.00    131.73    129.45    133.47    110.47    123.37    130.42
ILMN_1343292    146.32    142.71    161.47    161.04    126.72    123.00    131.73    129.45    133.47    110.47    123.37    130.42
ILMN_1343293    259.75    301.47    275.13    271.46    317.13    353.46    277.20    325.55    284.58    285.70    304.98    268.93
ILMN_1343294     73.82     73.29     65.64     72.57     74.63     72.87     85.44     83.64     86.72     71.58     69.31     82.14
ILMN_1651228    149.12    163.43    187.04    181.56    183.11    128.64    176.55    173.69    181.72    316.84    214.82    317.88
ILMN_1651229   1036.26    976.27    947.96    818.85    785.34    853.16   1023.08    951.63    709.39    856.48    846.67    932.35
ILMN_1651237    197.86    246.81    206.54    212.77    215.84    241.99    229.71    173.89    242.95    195.11    219.29    222.61
ILMN_1651254    152.10    151.04    144.70    169.72    167.76    165.94    169.19    159.90    184.89    151.28    143.96    180.83
ILMN_1651261    149.12    163.43    187.04    181.56    183.11    128.64    176.55    173.69    181.72    316.84    214.82    317.88
ILMN_1651262    225.23    284.67    308.46    293.74    228.57    194.03    237.91    254.24    374.52    233.38    417.27    320.19
ILMN_1651268     70.81     95.76     98.75    113.96     84.27     96.77     88.99     82.36    106.70     79.84     75.28     72.26
ILMN_1651278     74.18     77.68     87.89     97.07     86.83     74.37     88.05     69.56     90.29     93.03    111.52     95.70
ILMN_1651282   1791.96   1589.11   1774.30   1986.91   1734.38   1740.44   2562.24   1530.31   2777.14   3040.15   2661.15   3014.13
             GSM451222 GSM451223 GSM451224 GSM451225 GSM451226 GSM451227 GSM451228 GSM451229 GSM451230 GSM451231 GSM451232 GSM451233
ILMN_1343291    110.82    133.47    143.52    160.43    114.30    135.46    135.32    116.77    149.54    133.37    116.89    155.58
ILMN_1343292    110.82    133.47    143.52    160.43    114.30    135.46    135.32    116.77    149.54    133.37    116.89    155.58
ILMN_1343293    347.62    308.29    311.82    250.61    259.55    286.43    315.32    297.58    302.15    255.02    263.61    222.09
ILMN_1343294     72.95     75.68     79.60     72.81     70.85     73.16     66.48     61.71     64.67     72.42     73.10     99.75
ILMN_1651228    191.79    215.68    176.57    415.25    232.48    277.88    191.16    642.24    163.56    204.14    557.54    160.19
ILMN_1651229    981.69    956.78    792.59    650.33    849.36    976.77    710.40    904.32    920.72    770.56    867.57    747.52
ILMN_1651237    223.62    221.63    269.82    266.07    232.10    219.53    202.89    174.61    256.04    224.39    212.60    249.18
ILMN_1651254    157.89    155.43    119.27    145.17    153.11    140.87    177.77    123.45    148.04    117.62    148.07    178.35
ILMN_1651261    191.79    215.68    176.57    415.25    232.48    277.60    191.16    642.24    163.56    204.14    557.54    160.19
ILMN_1651262    240.49    240.42    253.80    252.57    277.25    262.93    291.16    185.23    248.27    261.61    235.65    230.46
ILMN_1651268    113.01     74.35     75.08     97.79     76.40     73.67     86.96     97.11     91.36     82.64     92.61     87.65
ILMN_1651278    124.06     98.24     79.69    101.65     77.93     78.36     78.55    132.41     84.85    104.32    145.57     93.07
ILMN_1651282   1678.74   1912.49   2225.04   1999.94   3136.89   2819.87   2633.90   1981.30   1938.51   2251.87   1805.98   1851.97
             GSM451234 GSM451235 GSM451236 GSM451237
ILMN_1343291    167.81    138.51    140.73    161.17
ILMN_1343292    167.81    138.51    140.73    161.17
ILMN_1343293    269.17    261.87    286.33    304.17
ILMN_1343294     85.17     84.89     81.15     85.68
ILMN_1651228    228.39    178.70    151.41    218.93
ILMN_1651229    821.36    699.58    674.15    953.21
ILMN_1651237    209.50    229.44    225.64    229.54
ILMN_1651254    152.45    146.86    150.57    155.82
ILMN_1651261    228.39    178.70    151.12    218.93
ILMN_1651262    255.80    236.14    254.53    271.65
ILMN_1651268    100.19     94.44     92.06     75.02
ILMN_1651278     81.73     79.83     77.63     82.86
ILMN_1651282   2167.65   2077.36   2077.36   2440.48
 [ reached getOption("max.print") -- omitted 11142 rows ]
#Active Smoking Dataset
pData(gseAS) ## print the sample information
fData(gseAS) ## print the gene annotation
exprs(gseAS) ## print the expression data
              GSM674181  GSM674182  GSM674183  GSM674184  GSM674185  GSM674186  GSM674187  GSM674188  GSM674189  GSM674190  GSM674191
ILMN_1343291 14.8619778 14.7910049 14.7452011 14.7910049 14.8619778 14.7452011 14.8619778 14.6982075 14.7452011 14.7910049 14.7452011
ILMN_1651209  2.5685167  2.7272693  2.7475569  2.6750045  2.5532888  3.3415974  2.4195101  2.6927972  2.7817207  2.2441842  3.2584289
ILMN_1651228  8.5750943  9.9841923 10.3281227  9.8260592 10.0326597  9.0887247 10.8615345 11.3055992 10.0466991 10.5095958 10.3484435
ILMN_1651229  3.1590667  4.1096401  4.5489735  5.2069581  5.0817526  4.4604426  4.1898441  4.2047952  4.5915581  4.4294000  4.3272872
ILMN_1651235  1.7496571  2.1460404  1.9005771  2.3356164  2.0435947  1.9749846  2.3473446  2.4599578  1.9248186  1.9696352  1.8733256
              GSM674192  GSM674193  GSM674194  GSM674195  GSM674196  GSM674197  GSM674198  GSM674199  GSM674200  GSM674201  GSM674202
ILMN_1343291 14.3158285 14.5259423 14.7910049 14.8619778 14.6982075 14.4652898 14.5764206 14.4869054 14.8619778 14.7452011 14.7910049
ILMN_1651209  3.3729830  2.7147483  2.9519653  2.5016719  2.0643223  2.7545884  2.5575992  2.5980040  2.0244837  2.5827687  2.8940409
ILMN_1651228 10.0200275  9.8842667 10.7143717 10.6503148 10.2273249  9.9799361 10.1677480  9.9179893 10.6673446 10.3621971 11.4263771
ILMN_1651229  4.0406611  3.8099323  4.5554201  4.6069612  4.0509786  3.8099323  4.5118417  4.2672160  4.5021940  4.1772376  3.4124302
ILMN_1651235  1.8907805  1.8003602  2.0608954  2.3280294  1.9153709  2.4077274  1.9532964  1.7104076  2.0458226  2.0820828  1.6283743
              GSM674203  GSM674204  GSM674205  GSM674206  GSM674207  GSM674208  GSM674209  GSM674210  GSM674211  GSM674212  GSM674213
ILMN_1343291 14.1302842 14.3464777 14.3653147 14.5499591 14.6651862 14.1758769 14.7452011 14.5499591 14.5499591 14.6982075 14.6319381
ILMN_1651209  2.1543775  3.3384963  2.7121567  2.0215363  2.3192907  2.0602498  2.6337253  2.9488517  2.2383876  2.4524280  2.2789914
ILMN_1651228 10.5980718 10.1702768  9.8600703 10.9399263 11.4553938 10.0200275  9.3211019 10.2602759 10.0662662 11.3539900 11.3594342
ILMN_1651229  4.1671320  3.8671932  3.0109870  4.0086356  3.7742856  2.7045066  3.2348003  4.7926620  3.8676837  4.2365312  4.5941497
ILMN_1651235  1.5184042  1.6027677  1.7192858  2.7088267  1.5315885  2.2193393  3.0533658  2.1313841  1.6761320  1.9036561  1.6141945
              GSM674214  GSM674215  GSM674216  GSM674217  GSM674218  GSM674219  GSM674220  GSM674221  GSM674222  GSM674223  GSM674224
ILMN_1343291 14.8619778 14.8619778 14.2060070 14.7910049 14.7910049 14.8619778 14.7910049 14.7910049 14.5259423 14.3464777 14.6027668
ILMN_1651209  2.7800397  3.2371026  2.9539295  2.9357204  3.2459192  2.2769161  2.8643361  2.3292605  3.0322662  1.7062384  1.4615467
ILMN_1651228 11.3262496 11.0983170 11.2868194 11.6558441 11.2092185 10.5909254 11.7766805 11.6396209 11.7184957 10.0888207 10.3388581
ILMN_1651229  4.8008259  4.9267999  5.2674562  4.0155367  3.9691965  4.7323616  4.8451105  3.8914343  4.6388481  2.6981938  3.2076198
ILMN_1651235  1.4401514  1.3687787  2.1066137  1.6991814  2.7388188  1.0317704  1.9215757  1.5905028  1.7750802  1.5192519  2.4095676
              GSM674225  GSM674226  GSM674227  GSM674228  GSM674229  GSM674230  GSM674231  GSM674232  GSM674233  GSM674234  GSM674235
ILMN_1343291 14.7452011 14.6027668 14.7910049 14.7452011 14.4869054 14.7452011 14.6982075 14.5077111 14.7910049 14.5259423 14.7910049
ILMN_1651209  2.4205234  2.2272267  2.7582861  2.9662652  2.1270319  3.1211454  3.4732736  2.7209212  1.5670327  2.5166910  2.8136225
ILMN_1651228 10.5737572 10.3586630 11.2746011 11.2092185 10.6336150 10.7897432 11.2018201 11.1907319 11.6487341 11.0501232 11.8929778
ILMN_1651229  5.5282177  4.6904697  3.1992837  3.7780043  3.6389730  4.6250598  3.8518855  4.5914539  4.0730380  4.0356761  4.6148738
ILMN_1651235  2.0107251  2.0951334  2.0884350  2.2512684  2.4399999  1.7953190  2.0742323  1.6963980  1.4932238  1.6530551  1.7861499
              GSM674236  GSM674237  GSM674238  GSM674239  GSM674240  GSM674241  GSM674242  GSM674243  GSM674244  GSM674245  GSM674282
ILMN_1343291 14.6651862 14.2209468 14.8619778 14.4002420 14.8619778 14.5077111 14.3464777 14.7910049 14.7452011 14.7452011 14.8669818
ILMN_1651209  2.6695269  3.5877183  2.6066791  1.9514989  1.9204960  2.1210264  2.5852612  1.3731196  3.0567458  3.0996575  2.8597060
ILMN_1651228 11.7156361 10.0649749 11.1792289 10.5115523  9.8454368 10.6162368  9.8474156  9.5614657 10.3972041 10.0738616  9.2438970
ILMN_1651229  4.2121943  4.4693053  4.2804220  4.4299211  4.5281000  4.6050552  5.3613444  1.8589038  5.0375551  4.8153558  6.5884598
ILMN_1651235  2.6358671  2.0348639  2.2910378  1.7740890  1.8108544  2.7827124  2.3606424  1.7602213  1.8334249  1.6556977  1.5598855
              GSM674283  GSM674284  GSM674285  GSM674286  GSM674287  GSM674288  GSM674289  GSM674290  GSM674291  GSM674292  GSM674293
ILMN_1343291 14.2970073 14.8669818 14.5485991 14.5846971 14.7446305 14.3937962 14.7446305 14.6776908 14.6300193 14.5846971 14.7446305
ILMN_1651209  2.7866525  2.2942225  3.4518428  2.6782817  2.6545643  2.5303211  2.8669747  2.6842813  3.5076923  2.5966956  2.2604187
ILMN_1651228  9.1212002  9.3065155  9.2038637  9.2365503  9.7389173  9.5730171  9.1671784  9.3560903  9.0109836  9.0606835  9.9839853
ILMN_1651229  5.5479582  6.2473030  6.3915213  5.6875967  6.2941456  6.8176207  6.1565746  6.3307417  6.2914905  6.8543444  6.5645643
ILMN_1651235  2.2866530  2.1405070  2.1935872  1.5613664  1.7418406  2.2222765  1.6514138  1.9616269  1.9590055  2.1656142  1.9890106
              GSM674294  GSM674295  GSM674296  GSM674297  GSM674298  GSM674299  GSM674300  GSM674301  GSM674302  GSM674303  GSM674304
ILMN_1343291 14.6776908 14.4514737 14.8669818 14.8669818 14.8669818 14.6300193 14.6776908 14.6300193 14.6300193 14.6300193 14.6776908
ILMN_1651209  2.4525984  3.2438927  1.8431472  2.1567333  2.0214230  3.3123641  2.1837161  1.9289795  2.3012542  2.2347472  2.7080298
ILMN_1651228  9.7595112  9.8516618 11.1372391 11.3671765 11.2337077  9.8965737 10.4857861 10.9318827 10.7136345 10.1932937  9.9702953
ILMN_1651229  6.3579337  7.5810176  5.5306939  6.5132096  6.2658574  6.9405233  6.4635283  6.3134180  6.2585382  6.5671119  6.0563209
ILMN_1651235  2.2772461  2.0772998  1.6588625  1.5962859  1.5520857  2.4321910  2.1481835  2.2113218  1.8018961  2.4649837  2.6024249
              GSM674305  GSM674306  GSM674307  GSM674308  GSM674309  GSM674310  GSM674311  GSM674312  GSM674313  GSM674314  GSM674315
ILMN_1343291 14.7446305 14.7446305 14.8669818 14.5846971 14.5485991 14.7446305 14.7446305 13.8342572 14.4514737 14.5485991 14.6776908
ILMN_1651209  2.1609801  1.5426242  2.4050770  3.1014624  2.1299504  2.6088141  1.4429639  3.3283915  2.2741790  1.4744680  2.1483135
ILMN_1651228 10.7783201 11.5179215 10.4411918 10.8776186  9.9227118 10.6815714 10.9839949 11.4211297 11.2639495 10.7601360 11.4019354
ILMN_1651229  6.1015973  6.2117883  6.1875568  6.3610525  6.5339310  5.9402849  6.3048743  7.6011659  7.1978414  6.6393796  6.6255985
ILMN_1651235  1.6621861  2.0765158  1.5297423  2.6610012  1.5736676  1.6086295  2.6409783  1.5370337  1.9262640  1.5446570  1.5507172
              GSM674316  GSM674317  GSM674318  GSM674319  GSM674320  GSM674321  GSM674322  GSM674323  GSM674324  GSM674325  GSM674326
ILMN_1343291 14.5846971 14.6776908 14.8669818 14.2540347 14.6776908 14.6300193 14.7446305 14.6776908 14.7446305 14.7446305 14.7446305
ILMN_1651209  2.3542759  2.5987051  2.4038210  3.2799448  3.3749177  2.7413456  2.8334551  2.9769641  1.8607884  2.0665267  2.2579338
ILMN_1651228 11.4507248 11.5553999 11.1253792 11.0279854 10.9890261  9.6940703 10.6254560 10.4638658 10.9291390 10.6254560 11.0316789
ILMN_1651229  6.1597562  7.0322198  5.9334322  7.3975591  6.9196361  6.7909868  6.8018210  6.2873643  6.1433642  6.2455196  5.9799070
ILMN_1651235  1.8525512  1.7992732  2.1137866  1.8829099  2.0555567  2.2086053  2.0375019  1.7909797  1.2741860  1.7572010  2.0349234
              GSM674327  GSM674328  GSM674329  GSM674330  GSM674331  GSM674332  GSM674333  GSM674334  GSM674335  GSM674344  GSM674345
ILMN_1343291 14.5485991 14.7446305 14.6776908 14.6776908 14.5485991 14.6300193 14.7446305 14.6776908 14.6300193 14.5381996 14.5780819
ILMN_1651209  2.4705036  2.3918427  2.0012014  1.9239242  2.1022741  2.2996707  2.9240841  2.9832345  2.4272538  1.8354051  2.8784357
ILMN_1651228 10.3563497 10.3221160 10.2452752  9.6459614 10.8800591 10.5515619 10.9005339 10.4876663 10.4465277 10.1531222 10.6507552
ILMN_1651229  5.9342262  6.8321071  6.7018967  5.7886166  5.7147863  5.2385398  5.7172206  5.5381003  6.3433512  4.1053476  5.1837752
ILMN_1651235  2.1994342  1.8815883  2.0649804  1.8985712  1.2508803  2.2151086  2.5775372  1.6296972  1.8795056  1.6792910  2.3277708
              GSM674346  GSM674347  GSM674348  GSM674349  GSM674350  GSM674351  GSM674352  GSM674353  GSM674354  GSM674355  GSM674356
ILMN_1343291 14.6763922 14.5381996 14.5381996 14.7432068 14.6763922 14.6763922 14.6763922 14.6763922 14.7432068 14.6205539 14.5780819
ILMN_1651209  3.0699665  3.3623307  3.0952438  2.7826015  3.1019396  2.3953646  3.1841707  2.3882802  2.1021650  3.4607306  3.1439099
ILMN_1651228 10.5703830 10.1575640  9.3771117 10.7811385 10.8424860 10.8424860 10.9626655 10.2534790 11.3199148 11.4385430 11.1683191
ILMN_1651229  4.6612206  4.8930973  5.0399211  5.2358327  4.6213188  4.7000349  4.6655129  4.5665047  4.6386040  5.5381361  4.5019196
ILMN_1651235  2.4591110  1.7208283  1.7852430  1.8534349  1.9293621  1.6148108  2.0706519  2.1453816  1.6197573  1.9987733  1.8334965
              GSM674357  GSM674358  GSM674359  GSM674360  GSM674361  GSM674362  GSM674363  GSM674364  GSM674365  GSM674366  GSM674367
ILMN_1343291 14.5100191 14.6763922 14.6763922 14.5780819 14.6763922 14.9304275 14.9304275 14.7432068 14.9304275 14.4750391 14.5100191
ILMN_1651209  2.6166347  2.5778365  2.9148343  3.3618320  3.7071059  2.4489487  2.5592007  4.0001492  2.8624496  2.7744766  1.8177584
ILMN_1651228 11.3729133 11.2800181 10.6453119 11.1308828 10.7372395 11.4162806 11.4347151 11.2240437 10.9346891 12.2331067 11.9884317
ILMN_1651229  4.6205709  5.7863155  4.4170681  4.9141539  4.8756530  3.6233818  4.3721628  5.8038052  4.7446543  5.0825770  5.5475251
ILMN_1651235  1.9391840  1.6764801  1.6000156  1.5291720  2.7411907  3.2669709  2.2647482  3.5263763  2.1603423  1.6808062  2.0878640
              GSM674368  GSM674369  GSM674370  GSM674371  GSM674372  GSM674373  GSM674374  GSM674375  GSM674376  GSM674377  GSM674378
ILMN_1343291 14.9304275 14.7432068 14.5381996 14.9304275 14.6763922 14.6205539 14.5381996 14.7432068 14.7432068 14.7432068 14.7432068
ILMN_1651209  3.6543929  2.9524580  2.4085480  2.5198109  3.3497347  3.0028326  2.9638433  3.1105393  3.6443485  2.7389128  3.4080067
ILMN_1651228 11.8933188 11.9587291 12.1378779 11.3982976 11.2240437 10.0595683 10.7086102 11.7148977 11.7682867 11.4497738 11.1627601
ILMN_1651229  5.0648312  4.9738923  5.1901189  4.7324017  4.9295341  5.3648923  5.4440649  5.4742133  5.7344326  5.5969800  5.2254154
ILMN_1651235  1.7133883  2.1495297  1.3106208  2.1421694  2.0203264  2.0501583  1.8027632  2.1474522  1.5732898  2.1181844  2.0708921
              GSM674379  GSM674380  GSM674381  GSM674382  GSM674383  GSM674384  GSM674385  GSM674386  GSM674387  GSM674388  GSM674389
ILMN_1343291 14.6205539 14.6763922 14.6763922 14.5780819 14.7432068 14.7432068 14.7432068 14.7432068 14.4131767 14.9304275 14.6205539
ILMN_1651209  2.4236271  2.8614553  2.8988961  3.0119205  3.0141082  3.0583510  2.1811141  2.9350100  2.4008032  2.3358918  2.8239546
ILMN_1651228 11.8504341 11.5707499 11.6264803 12.0488571 11.4310339 11.2800181 10.3702607 10.9626655 11.5541332 10.6322653 10.9612812
ILMN_1651229  5.9543351  5.9582613  5.1454887  5.9337991  4.2399777  5.7353076  4.7147375  6.2045911  5.6519743  5.0966169  5.3418335
ILMN_1651235  1.7872678  2.2265947  1.6255226  2.1713515  2.8554764  1.9505383  2.0039577  1.6785918  1.5637831  1.6518372  1.4480261
              GSM674390  GSM674391  GSM674392  GSM674393  GSM674394  GSM674395  GSM674396  GSM674397  GSM674398  GSM674399  GSM674400
ILMN_1343291 14.6205539 14.6205539 14.7432068 14.7432068 14.7432068 14.7432068 14.6763922 14.7432068 14.6763922 14.7432068 14.7432068
ILMN_1651209  3.2664697  2.8730511  2.3035390  2.6139301  4.2937556  3.2158692  3.6507478  2.0020956  2.2201926  3.0632576  3.2441759
ILMN_1651228 11.3630119 11.9404693 11.4454111 10.8329959 10.6136104 10.5212532 10.7275257 11.0056648 10.3258850 10.5761667 10.6782012
ILMN_1651229  5.6196229  6.5421974  4.6741590  5.0555842  5.4242350  5.1598772  5.7181292  5.0241896  5.4880515  6.3289077  4.4259048
ILMN_1651235  2.1484274  2.2507025  2.3818827  1.7530639  1.8777645  1.8637018  1.7980119  1.9933630  1.9427921  1.8303903  1.9530155
              GSM674401  GSM674402  GSM674403  GSM674404  GSM674405  GSM674406  GSM674407
ILMN_1343291 14.7432068 14.7432068 14.6763922 14.7432068 14.7432068 14.7432068 14.7432068
ILMN_1651209  3.3487016  3.4401422  2.2405803  3.2349158  2.2318294  1.9505383  2.3713452
ILMN_1651228 10.5435433 10.6369493 11.4602394 10.7513246 10.6525819 11.4057107 11.7872534
ILMN_1651229  5.2381301  4.6090295  3.6550872  5.7181292  5.6076725  5.3782176  6.0621664
ILMN_1651235  1.3498251  1.9116361  1.9097331  2.4694678  1.8778786  1.3277622  1.3969692
 [ reached getOption("max.print") -- omitted 24521 rows ]

The summary function can then be used to print the distributions.

## exprs get the expression levels as a data frame and get the distribution
summary(exprs(gsePS))
   GSM451162         GSM451163         GSM451164         GSM451165        GSM451166         GSM451167         GSM451168      
 Min.   :  69.95   Min.   :  67.51   Min.   :  70.78   Min.   :  67.6   Min.   :  70.18   Min.   :  69.91   Min.   :  70.34  
 1st Qu.: 117.79   1st Qu.: 103.96   1st Qu.:  98.88   1st Qu.: 100.1   1st Qu.:  93.77   1st Qu.: 101.57   1st Qu.: 105.22  
 Median : 214.33   Median : 200.89   Median : 211.24   Median : 197.9   Median : 181.96   Median : 215.51   Median : 207.33  
 Mean   : 644.97   Mean   : 564.37   Mean   : 604.19   Mean   : 651.3   Mean   : 589.80   Mean   : 641.00   Mean   : 607.12  
 3rd Qu.: 431.17   3rd Qu.: 376.59   3rd Qu.: 362.47   3rd Qu.: 455.1   3rd Qu.: 409.92   3rd Qu.: 484.91   3rd Qu.: 438.07  
 Max.   :4577.08   Max.   :4188.76   Max.   :4302.45   Max.   :4397.3   Max.   :3648.54   Max.   :3957.03   Max.   :3854.98  
   GSM451169         GSM451170         GSM451171         GSM451172         GSM451173         GSM451174         GSM451175      
 Min.   :  69.59   Min.   :  62.87   Min.   :  62.36   Min.   :  71.45   Min.   :  61.34   Min.   :  65.06   Min.   :  70.19  
 1st Qu.: 105.92   1st Qu.:  91.64   1st Qu.:  99.31   1st Qu.: 116.12   1st Qu.: 104.04   1st Qu.: 101.23   1st Qu.: 101.18  
 Median : 217.10   Median : 246.73   Median : 226.75   Median : 233.95   Median : 225.36   Median : 204.28   Median : 182.75  
 Mean   : 576.58   Mean   : 628.23   Mean   : 545.69   Mean   : 663.25   Mean   : 699.44   Mean   : 663.20   Mean   : 639.25  
 3rd Qu.: 371.72   3rd Qu.: 416.42   3rd Qu.: 403.28   3rd Qu.: 361.16   3rd Qu.: 455.31   3rd Qu.: 390.17   3rd Qu.: 809.12  
 Max.   :4029.33   Max.   :4037.12   Max.   :3304.50   Max.   :4749.54   Max.   :4250.30   Max.   :4311.29   Max.   :4176.00  
   GSM451176         GSM451177         GSM451178         GSM451179         GSM451180         GSM451181         GSM451182      
 Min.   :  69.36   Min.   :  67.49   Min.   :  65.97   Min.   :  66.92   Min.   :  65.88   Min.   :  67.17   Min.   :  64.79  
 1st Qu.:  99.88   1st Qu.:  90.63   1st Qu.:  89.68   1st Qu.:  98.80   1st Qu.:  92.52   1st Qu.:  93.57   1st Qu.:  95.19  
 Median : 229.15   Median : 189.11   Median : 227.74   Median : 231.42   Median : 199.26   Median : 191.11   Median : 195.49  
 Mean   : 660.73   Mean   : 676.09   Mean   : 690.10   Mean   : 685.89   Mean   : 665.28   Mean   : 624.51   Mean   : 631.34  
 3rd Qu.: 469.75   3rd Qu.: 476.25   3rd Qu.: 444.14   3rd Qu.: 403.84   3rd Qu.: 490.42   3rd Qu.: 484.70   3rd Qu.: 411.67  
 Max.   :3994.13   Max.   :4219.00   Max.   :4198.77   Max.   :4188.76   Max.   :4188.76   Max.   :3656.17   Max.   :3490.05  
   GSM451183         GSM451184         GSM451185         GSM451186         GSM451187         GSM451188         GSM451189     
 Min.   :  61.36   Min.   :  65.14   Min.   :  66.22   Min.   :  66.51   Min.   :  69.99   Min.   :  64.27   Min.   :  64.1  
 1st Qu.: 114.59   1st Qu.:  98.75   1st Qu.: 117.43   1st Qu.:  99.41   1st Qu.: 104.40   1st Qu.:  95.78   1st Qu.: 106.0  
 Median : 184.17   Median : 224.58   Median : 209.70   Median : 241.14   Median : 171.58   Median : 190.03   Median : 214.8  
 Mean   : 656.13   Mean   : 693.17   Mean   : 680.92   Mean   : 636.53   Mean   : 609.69   Mean   : 677.53   Mean   : 666.9  
 3rd Qu.: 559.41   3rd Qu.: 463.03   3rd Qu.: 778.51   3rd Qu.: 779.19   3rd Qu.: 509.14   3rd Qu.: 433.82   3rd Qu.: 403.4  
 Max.   :4291.82   Max.   :4749.54   Max.   :4188.76   Max.   :3535.39   Max.   :3870.51   Max.   :4924.12   Max.   :4291.8  
   GSM451190         GSM451191         GSM451192         GSM451193         GSM451194         GSM451195         GSM451196      
 Min.   :  69.60   Min.   :  70.24   Min.   :  68.53   Min.   :  66.73   Min.   :  61.26   Min.   :  61.30   Min.   :  53.27  
 1st Qu.:  99.86   1st Qu.: 111.26   1st Qu.: 107.76   1st Qu.:  84.42   1st Qu.: 102.55   1st Qu.:  98.72   1st Qu.:  94.84  
 Median : 221.34   Median : 219.72   Median : 253.14   Median : 195.37   Median : 220.49   Median : 232.66   Median : 203.67  
 Mean   : 638.54   Mean   : 618.70   Mean   : 587.92   Mean   : 701.29   Mean   : 710.22   Mean   : 712.88   Mean   : 565.86  
 3rd Qu.: 467.60   3rd Qu.: 495.56   3rd Qu.: 554.95   3rd Qu.: 590.93   3rd Qu.: 583.57   3rd Qu.: 585.55   3rd Qu.: 455.84  
 Max.   :3725.19   Max.   :3921.81   Max.   :3200.93   Max.   :4749.54   Max.   :5142.26   Max.   :4773.32   Max.   :3040.15  
   GSM451197        GSM451198         GSM451199         GSM451200         GSM451201         GSM451202         GSM451203      
 Min.   :  59.1   Min.   :  61.68   Min.   :  63.07   Min.   :  66.50   Min.   :  61.48   Min.   :  75.92   Min.   :  67.25  
 1st Qu.: 110.8   1st Qu.: 118.11   1st Qu.: 107.69   1st Qu.:  98.88   1st Qu.: 148.79   1st Qu.: 107.64   1st Qu.:  95.67  
 Median : 233.0   Median : 235.83   Median : 238.38   Median : 230.20   Median : 251.14   Median : 232.94   Median : 222.82  
 Mean   : 688.6   Mean   : 741.01   Mean   : 700.92   Mean   : 688.22   Mean   : 722.32   Mean   : 634.33   Mean   : 598.12  
 3rd Qu.: 506.3   3rd Qu.: 634.35   3rd Qu.: 548.01   3rd Qu.: 553.47   3rd Qu.: 575.77   3rd Qu.: 407.12   3rd Qu.: 430.02  
 Max.   :5158.4   Max.   :5508.95   Max.   :4761.82   Max.   :4590.00   Max.   :4938.49   Max.   :3520.58   Max.   :3273.86  
   GSM451204         GSM451205         GSM451206         GSM451207        GSM451208         GSM451209         GSM451210      
 Min.   :  68.75   Min.   :  65.36   Min.   :  62.60   Min.   :  72.0   Min.   :  63.73   Min.   :  60.82   Min.   :  70.81  
 1st Qu.: 104.57   1st Qu.: 108.83   1st Qu.:  93.74   1st Qu.: 103.8   1st Qu.: 106.05   1st Qu.:  98.42   1st Qu.:  90.03  
 Median : 224.58   Median : 192.83   Median : 197.66   Median : 204.1   Median : 194.78   Median : 218.86   Median : 197.86  
 Mean   : 599.24   Mean   : 591.81   Mean   : 585.37   Mean   : 586.9   Mean   : 606.90   Mean   : 671.52   Mean   : 611.38  
 3rd Qu.: 426.03   3rd Qu.: 438.07   3rd Qu.: 500.13   3rd Qu.: 434.5   3rd Qu.: 412.50   3rd Qu.: 398.99   3rd Qu.: 433.24  
 Max.   :3804.90   Max.   :3563.62   Max.   :3297.63   Max.   :3490.1   Max.   :3448.61   Max.   :4076.08   Max.   :3628.08  
   GSM451211         GSM451212         GSM451213         GSM451214         GSM451215         GSM451216         GSM451217      
 Min.   :  73.29   Min.   :  63.02   Min.   :  57.33   Min.   :  70.57   Min.   :  72.87   Min.   :  67.06   Min.   :  65.61  
 1st Qu.:  95.76   1st Qu.:  98.75   1st Qu.: 108.16   1st Qu.: 100.78   1st Qu.:  90.17   1st Qu.:  88.54   1st Qu.:  99.49  
 Median : 212.77   Median : 206.51   Median : 212.77   Median : 215.84   Median : 194.03   Median : 210.41   Median : 187.98  
 Mean   : 567.80   Mean   : 605.02   Mean   : 604.00   Mean   : 640.74   Mean   : 612.08   Mean   : 633.44   Mean   : 580.17  
 3rd Qu.: 413.64   3rd Qu.: 474.43   3rd Qu.: 469.95   3rd Qu.: 447.11   3rd Qu.: 453.41   3rd Qu.: 392.24   3rd Qu.: 414.13  
 Max.   :3252.03   Max.   :3498.98   Max.   :3436.55   Max.   :3930.29   Max.   :3741.04   Max.   :3614.88   Max.   :3443.62  
   GSM451218         GSM451219         GSM451220         GSM451221         GSM451222         GSM451223         GSM451224      
 Min.   :  62.19   Min.   :  71.58   Min.   :  62.11   Min.   :  72.26   Min.   :  59.93   Min.   :  66.73   Min.   :  75.08  
 1st Qu.: 104.74   1st Qu.: 101.94   1st Qu.: 111.52   1st Qu.:  98.96   1st Qu.: 110.82   1st Qu.: 116.42   1st Qu.:  95.86  
 Median : 184.89   Median : 233.38   Median : 219.29   Median : 268.93   Median : 169.99   Median : 221.63   Median : 253.80  
 Mean   : 695.01   Mean   : 681.32   Mean   : 682.65   Mean   : 762.76   Mean   : 613.57   Mean   : 673.24   Mean   : 672.81  
 3rd Qu.: 454.08   3rd Qu.: 444.60   3rd Qu.: 417.72   3rd Qu.: 425.01   3rd Qu.: 688.76   3rd Qu.: 450.34   3rd Qu.: 485.91  
 Max.   :4837.99   Max.   :4094.56   Max.   :3974.74   Max.   :5108.48   Max.   :3475.10   Max.   :3887.32   Max.   :3887.32  
   GSM451225         GSM451226         GSM451227         GSM451228         GSM451229         GSM451230         GSM451231      
 Min.   :  58.24   Min.   :  69.74   Min.   :  67.13   Min.   :  58.13   Min.   :  59.55   Min.   :  63.16   Min.   :  68.70  
 1st Qu.: 101.65   1st Qu.:  89.91   1st Qu.: 100.29   1st Qu.:  94.86   1st Qu.:  97.11   1st Qu.:  92.31   1st Qu.:  95.22  
 Median : 250.61   Median : 232.48   Median : 262.93   Median : 202.89   Median : 185.23   Median : 163.56   Median : 204.14  
 Mean   : 617.60   Mean   : 701.49   Mean   : 703.98   Mean   : 668.20   Mean   : 645.63   Mean   : 640.65   Mean   : 618.18  
 3rd Qu.: 482.18   3rd Qu.: 592.00   3rd Qu.: 498.59   3rd Qu.: 493.10   3rd Qu.: 642.24   3rd Qu.: 479.84   3rd Qu.: 435.79  
 Max.   :3634.31   Max.   :3732.93   Max.   :3870.51   Max.   :3648.54   Max.   :3570.66   Max.   :4047.49   Max.   :3605.82  
   GSM451232         GSM451233         GSM451234         GSM451235         GSM451236         GSM451237      
 Min.   :  56.71   Min.   :  72.40   Min.   :  59.27   Min.   :  51.17   Min.   :  73.63   Min.   :  63.67  
 1st Qu.: 103.03   1st Qu.:  99.75   1st Qu.: 117.73   1st Qu.: 104.55   1st Qu.:  91.22   1st Qu.:  92.15  
 Median : 213.68   Median : 178.35   Median : 209.50   Median : 201.05   Median : 177.11   Median : 218.93  
 Mean   : 625.45   Mean   : 591.06   Mean   : 643.75   Mean   : 604.08   Mean   : 570.28   Mean   : 624.31  
 3rd Qu.: 557.54   3rd Qu.: 416.27   3rd Qu.: 434.62   3rd Qu.: 396.64   3rd Qu.: 413.88   3rd Qu.: 415.70  
 Max.   :3732.93   Max.   :3382.05   Max.   :4163.00   Max.   :4057.80   Max.   :3291.24   Max.   :3831.09  
summary(exprs(gseAS))
   GSM674181         GSM674182         GSM674183         GSM674184         GSM674185         GSM674186         GSM674187      
 Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453  
 1st Qu.: 1.8251   1st Qu.: 1.8245   1st Qu.: 1.8257   1st Qu.: 1.8219   1st Qu.: 1.8270   1st Qu.: 1.8291   1st Qu.: 1.8257  
 Median : 2.9376   Median : 2.9407   Median : 2.9384   Median : 2.9367   Median : 2.9384   Median : 2.9366   Median : 2.9398  
 Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1618  
 3rd Qu.: 6.1472   3rd Qu.: 6.1475   3rd Qu.: 6.1470   3rd Qu.: 6.1470   3rd Qu.: 6.1476   3rd Qu.: 6.1467   3rd Qu.: 6.1471  
   GSM674188         GSM674189         GSM674190         GSM674191         GSM674192         GSM674193         GSM674194      
 Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5718   Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453  
 1st Qu.: 1.8199   1st Qu.: 1.8218   1st Qu.: 1.8303   1st Qu.: 1.8240   1st Qu.: 1.8229   1st Qu.: 1.8241   1st Qu.: 1.8258  
 Median : 2.9376   Median : 2.9331   Median : 2.9410   Median : 2.9398   Median : 2.9390   Median : 2.9375   Median : 2.9375  
 Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1617   Mean   : 4.1617   Mean   : 4.1618   Mean   : 4.1618  
 3rd Qu.: 6.1475   3rd Qu.: 6.1472   3rd Qu.: 6.1467   3rd Qu.: 6.1467   3rd Qu.: 6.1472   3rd Qu.: 6.1461   3rd Qu.: 6.1471  
   GSM674195         GSM674196         GSM674197         GSM674198         GSM674199         GSM674200         GSM674201      
 Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5718   Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453  
 1st Qu.: 1.8234   1st Qu.: 1.8266   1st Qu.: 1.8257   1st Qu.: 1.8270   1st Qu.: 1.8278   1st Qu.: 1.8276   1st Qu.: 1.8251  
 Median : 2.9398   Median : 2.9390   Median : 2.9385   Median : 2.9395   Median : 2.9321   Median : 2.9392   Median : 2.9414  
 Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1617   Mean   : 4.1618  
 3rd Qu.: 6.1467   3rd Qu.: 6.1472   3rd Qu.: 6.1470   3rd Qu.: 6.1474   3rd Qu.: 6.1472   3rd Qu.: 6.1471   3rd Qu.: 6.1464  
   GSM674202         GSM674203         GSM674204         GSM674205         GSM674206         GSM674207         GSM674208      
 Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5718   Min.   : 0.5453  
 1st Qu.: 1.8238   1st Qu.: 1.8246   1st Qu.: 1.8246   1st Qu.: 1.8251   1st Qu.: 1.8217   1st Qu.: 1.8258   1st Qu.: 1.8258  
 Median : 2.9331   Median : 2.9335   Median : 2.9410   Median : 2.9376   Median : 2.9338   Median : 2.9374   Median : 2.9400  
 Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1616   Mean   : 4.1618   Mean   : 4.1618  
 3rd Qu.: 6.1465   3rd Qu.: 6.1475   3rd Qu.: 6.1475   3rd Qu.: 6.1470   3rd Qu.: 6.1464   3rd Qu.: 6.1467   3rd Qu.: 6.1453  
   GSM674209         GSM674210         GSM674211         GSM674212         GSM674213         GSM674214         GSM674215      
 Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453  
 1st Qu.: 1.8254   1st Qu.: 1.8250   1st Qu.: 1.8288   1st Qu.: 1.8278   1st Qu.: 1.8253   1st Qu.: 1.8275   1st Qu.: 1.8288  
 Median : 2.9387   Median : 2.9376   Median : 2.9411   Median : 2.9365   Median : 2.9373   Median : 2.9377   Median : 2.9396  
 Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1618  
 3rd Qu.: 6.1486   3rd Qu.: 6.1472   3rd Qu.: 6.1475   3rd Qu.: 6.1472   3rd Qu.: 6.1467   3rd Qu.: 6.1470   3rd Qu.: 6.1467  
   GSM674216         GSM674217         GSM674218         GSM674219         GSM674220         GSM674221         GSM674222      
 Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453  
 1st Qu.: 1.8218   1st Qu.: 1.8285   1st Qu.: 1.8187   1st Qu.: 1.8225   1st Qu.: 1.8270   1st Qu.: 1.8230   1st Qu.: 1.8312  
 Median : 2.9305   Median : 2.9357   Median : 2.9446   Median : 2.9376   Median : 2.9361   Median : 2.9375   Median : 2.9364  
 Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1617   Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1618  
 3rd Qu.: 6.1478   3rd Qu.: 6.1470   3rd Qu.: 6.1480   3rd Qu.: 6.1472   3rd Qu.: 6.1467   3rd Qu.: 6.1471   3rd Qu.: 6.1478  
   GSM674223         GSM674224         GSM674225         GSM674226         GSM674227         GSM674228         GSM674229      
 Min.   : 0.5718   Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453  
 1st Qu.: 1.8200   1st Qu.: 1.8316   1st Qu.: 1.8258   1st Qu.: 1.8344   1st Qu.: 1.8212   1st Qu.: 1.8203   1st Qu.: 1.8218  
 Median : 2.9396   Median : 2.9355   Median : 2.9329   Median : 2.9474   Median : 2.9355   Median : 2.9292   Median : 2.9454  
 Mean   : 4.1617   Mean   : 4.1617   Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1618  
 3rd Qu.: 6.1479   3rd Qu.: 6.1450   3rd Qu.: 6.1467   3rd Qu.: 6.1470   3rd Qu.: 6.1461   3rd Qu.: 6.1450   3rd Qu.: 6.1475  
   GSM674230         GSM674231         GSM674232         GSM674233         GSM674234         GSM674235         GSM674236      
 Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453  
 1st Qu.: 1.8251   1st Qu.: 1.8305   1st Qu.: 1.8223   1st Qu.: 1.8200   1st Qu.: 1.8266   1st Qu.: 1.8305   1st Qu.: 1.8218  
 Median : 2.9375   Median : 2.9462   Median : 2.9298   Median : 2.9413   Median : 2.9305   Median : 2.9411   Median : 2.9387  
 Mean   : 4.1615   Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1618  
 3rd Qu.: 6.1478   3rd Qu.: 6.1476   3rd Qu.: 6.1472   3rd Qu.: 6.1470   3rd Qu.: 6.1470   3rd Qu.: 6.1472   3rd Qu.: 6.1480  
   GSM674237         GSM674238         GSM674239         GSM674240         GSM674241         GSM674242         GSM674243      
 Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5453  
 1st Qu.: 1.8258   1st Qu.: 1.8200   1st Qu.: 1.8200   1st Qu.: 1.8266   1st Qu.: 1.8266   1st Qu.: 1.8305   1st Qu.: 1.8212  
 Median : 2.9409   Median : 2.9297   Median : 2.9392   Median : 2.9344   Median : 2.9364   Median : 2.9439   Median : 2.9285  
 Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.1617  
 3rd Qu.: 6.1467   3rd Qu.: 6.1472   3rd Qu.: 6.1470   3rd Qu.: 6.1467   3rd Qu.: 6.1475   3rd Qu.: 6.1472   3rd Qu.: 6.1480  
   GSM674244         GSM674245         GSM674282         GSM674283         GSM674284         GSM674285         GSM674286      
 Min.   : 0.5453   Min.   : 0.5453   Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5395   Min.   : 0.5107   Min.   : 0.5107  
 1st Qu.: 1.8224   1st Qu.: 1.8217   1st Qu.: 1.8407   1st Qu.: 1.8439   1st Qu.: 1.8418   1st Qu.: 1.8390   1st Qu.: 1.8381  
 Median : 2.9457   Median : 2.9305   Median : 3.1571   Median : 3.1558   Median : 3.1559   Median : 3.1539   Median : 3.1579  
 Mean   : 4.1618   Mean   : 4.1618   Mean   : 4.2616   Mean   : 4.2616   Mean   : 4.2617   Mean   : 4.2617   Mean   : 4.2617  
 3rd Qu.: 6.1472   3rd Qu.: 6.1471   3rd Qu.: 6.3833   3rd Qu.: 6.3834   3rd Qu.: 6.3837   3rd Qu.: 6.3832   3rd Qu.: 6.3832  
   GSM674287         GSM674288         GSM674289         GSM674290         GSM674291         GSM674292         GSM674293      
 Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5107  
 1st Qu.: 1.8372   1st Qu.: 1.8444   1st Qu.: 1.8407   1st Qu.: 1.8400   1st Qu.: 1.8445   1st Qu.: 1.8384   1st Qu.: 1.8431  
 Median : 3.1560   Median : 3.1559   Median : 3.1520   Median : 3.1573   Median : 3.1583   Median : 3.1517   Median : 3.1578  
 Mean   : 4.2617   Mean   : 4.2616   Mean   : 4.2617   Mean   : 4.2617   Mean   : 4.2617   Mean   : 4.2617   Mean   : 4.2616  
 3rd Qu.: 6.3837   3rd Qu.: 6.3835   3rd Qu.: 6.3838   3rd Qu.: 6.3832   3rd Qu.: 6.3832   3rd Qu.: 6.3837   3rd Qu.: 6.3839  
   GSM674294         GSM674295         GSM674296         GSM674297         GSM674298         GSM674299         GSM674300      
 Min.   : 0.5107   Min.   : 0.5395   Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5107  
 1st Qu.: 1.8481   1st Qu.: 1.8400   1st Qu.: 1.8431   1st Qu.: 1.8445   1st Qu.: 1.8445   1st Qu.: 1.8405   1st Qu.: 1.8393  
 Median : 3.1521   Median : 3.1572   Median : 3.1557   Median : 3.1573   Median : 3.1562   Median : 3.1558   Median : 3.1572  
 Mean   : 4.2617   Mean   : 4.2617   Mean   : 4.2617   Mean   : 4.2616   Mean   : 4.2616   Mean   : 4.2616   Mean   : 4.2616  
 3rd Qu.: 6.3837   3rd Qu.: 6.3832   3rd Qu.: 6.3837   3rd Qu.: 6.3834   3rd Qu.: 6.3830   3rd Qu.: 6.3837   3rd Qu.: 6.3835  
   GSM674301         GSM674302         GSM674303         GSM674304         GSM674305         GSM674306         GSM674307      
 Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5107  
 1st Qu.: 1.8462   1st Qu.: 1.8441   1st Qu.: 1.8362   1st Qu.: 1.8405   1st Qu.: 1.8400   1st Qu.: 1.8431   1st Qu.: 1.8445  
 Median : 3.1574   Median : 3.1522   Median : 3.1629   Median : 3.1505   Median : 3.1579   Median : 3.1523   Median : 3.1562  
 Mean   : 4.2616   Mean   : 4.2616   Mean   : 4.2616   Mean   : 4.2616   Mean   : 4.2617   Mean   : 4.2617   Mean   : 4.2616  
 3rd Qu.: 6.3840   3rd Qu.: 6.3830   3rd Qu.: 6.3834   3rd Qu.: 6.3846   3rd Qu.: 6.3821   3rd Qu.: 6.3832   3rd Qu.: 6.3840  
   GSM674308         GSM674309         GSM674310         GSM674311         GSM674312         GSM674313         GSM674314      
 Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5395   Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5395  
 1st Qu.: 1.8385   1st Qu.: 1.8393   1st Qu.: 1.8361   1st Qu.: 1.8441   1st Qu.: 1.8489   1st Qu.: 1.8484   1st Qu.: 1.8413  
 Median : 3.1521   Median : 3.1559   Median : 3.1559   Median : 3.1539   Median : 3.1573   Median : 3.1591   Median : 3.1557  
 Mean   : 4.2616   Mean   : 4.2617   Mean   : 4.2617   Mean   : 4.2616   Mean   : 4.2616   Mean   : 4.2616   Mean   : 4.2616  
 3rd Qu.: 6.3821   3rd Qu.: 6.3832   3rd Qu.: 6.3834   3rd Qu.: 6.3832   3rd Qu.: 6.3837   3rd Qu.: 6.3837   3rd Qu.: 6.3827  
   GSM674315         GSM674316         GSM674317         GSM674318         GSM674319         GSM674320         GSM674321      
 Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5107  
 1st Qu.: 1.8400   1st Qu.: 1.8400   1st Qu.: 1.8347   1st Qu.: 1.8445   1st Qu.: 1.8452   1st Qu.: 1.8477   1st Qu.: 1.8337  
 Median : 3.1523   Median : 3.1586   Median : 3.1516   Median : 3.1560   Median : 3.1633   Median : 3.1588   Median : 3.1562  
 Mean   : 4.2617   Mean   : 4.2617   Mean   : 4.2617   Mean   : 4.2617   Mean   : 4.2616   Mean   : 4.2617   Mean   : 4.2616  
 3rd Qu.: 6.3832   3rd Qu.: 6.3832   3rd Qu.: 6.3834   3rd Qu.: 6.3840   3rd Qu.: 6.3832   3rd Qu.: 6.3840   3rd Qu.: 6.3845  
   GSM674322         GSM674323         GSM674324         GSM674325         GSM674326         GSM674327         GSM674328      
 Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5107  
 1st Qu.: 1.8473   1st Qu.: 1.8447   1st Qu.: 1.8395   1st Qu.: 1.8443   1st Qu.: 1.8498   1st Qu.: 1.8486   1st Qu.: 1.8455  
 Median : 3.1586   Median : 3.1543   Median : 3.1536   Median : 3.1604   Median : 3.1522   Median : 3.1578   Median : 3.1534  
 Mean   : 4.2616   Mean   : 4.2617   Mean   : 4.2617   Mean   : 4.2616   Mean   : 4.2617   Mean   : 4.2617   Mean   : 4.2616  
 3rd Qu.: 6.3832   3rd Qu.: 6.3827   3rd Qu.: 6.3832   3rd Qu.: 6.3846   3rd Qu.: 6.3832   3rd Qu.: 6.3843   3rd Qu.: 6.3825  
   GSM674329         GSM674330         GSM674331         GSM674332         GSM674333         GSM674334         GSM674335      
 Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5107   Min.   : 0.5107  
 1st Qu.: 1.8502   1st Qu.: 1.8413   1st Qu.: 1.8385   1st Qu.: 1.8357   1st Qu.: 1.8467   1st Qu.: 1.8467   1st Qu.: 1.8326  
 Median : 3.1559   Median : 3.1512   Median : 3.1504   Median : 3.1516   Median : 3.1629   Median : 3.1591   Median : 3.1628  
 Mean   : 4.2616   Mean   : 4.2617   Mean   : 4.2617   Mean   : 4.2617   Mean   : 4.2617   Mean   : 4.2617   Mean   : 4.2616  
 3rd Qu.: 6.3821   3rd Qu.: 6.3830   3rd Qu.: 6.3837   3rd Qu.: 6.3851   3rd Qu.: 6.3830   3rd Qu.: 6.3832   3rd Qu.: 6.3830  
   GSM674344         GSM674345         GSM674346         GSM674347         GSM674348         GSM674349         GSM674350      
 Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5757   Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477  
 1st Qu.: 1.8533   1st Qu.: 1.8561   1st Qu.: 1.8517   1st Qu.: 1.8557   1st Qu.: 1.8578   1st Qu.: 1.8534   1st Qu.: 1.8498  
 Median : 3.1006   Median : 3.1004   Median : 3.0993   Median : 3.1058   Median : 3.1034   Median : 3.0996   Median : 3.1019  
 Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540  
 3rd Qu.: 6.3895   3rd Qu.: 6.3890   3rd Qu.: 6.3892   3rd Qu.: 6.3898   3rd Qu.: 6.3893   3rd Qu.: 6.3884   3rd Qu.: 6.3886  
   GSM674351         GSM674352         GSM674353         GSM674354         GSM674355         GSM674356         GSM674357      
 Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5757   Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477  
 1st Qu.: 1.8519   1st Qu.: 1.8540   1st Qu.: 1.8535   1st Qu.: 1.8558   1st Qu.: 1.8567   1st Qu.: 1.8522   1st Qu.: 1.8506  
 Median : 3.0965   Median : 3.1025   Median : 3.0976   Median : 3.0954   Median : 3.0997   Median : 3.0985   Median : 3.1046  
 Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540  
 3rd Qu.: 6.3894   3rd Qu.: 6.3881   3rd Qu.: 6.3879   3rd Qu.: 6.3890   3rd Qu.: 6.3892   3rd Qu.: 6.3894   3rd Qu.: 6.3893  
   GSM674358         GSM674359         GSM674360         GSM674361         GSM674362         GSM674363         GSM674364      
 Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477  
 1st Qu.: 1.8575   1st Qu.: 1.8518   1st Qu.: 1.8497   1st Qu.: 1.8591   1st Qu.: 1.8515   1st Qu.: 1.8594   1st Qu.: 1.8580  
 Median : 3.1057   Median : 3.0993   Median : 3.1057   Median : 3.0975   Median : 3.1059   Median : 3.1034   Median : 3.1044  
 Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540  
 3rd Qu.: 6.3895   3rd Qu.: 6.3891   3rd Qu.: 6.3895   3rd Qu.: 6.3893   3rd Qu.: 6.3884   3rd Qu.: 6.3895   3rd Qu.: 6.3906  
   GSM674365         GSM674366         GSM674367         GSM674368         GSM674369         GSM674370         GSM674371      
 Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477  
 1st Qu.: 1.8563   1st Qu.: 1.8538   1st Qu.: 1.8574   1st Qu.: 1.8578   1st Qu.: 1.8567   1st Qu.: 1.8547   1st Qu.: 1.8579  
 Median : 3.1001   Median : 3.0991   Median : 3.0979   Median : 3.0993   Median : 3.0945   Median : 3.1006   Median : 3.0996  
 Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540  
 3rd Qu.: 6.3890   3rd Qu.: 6.3897   3rd Qu.: 6.3893   3rd Qu.: 6.3894   3rd Qu.: 6.3895   3rd Qu.: 6.3893   3rd Qu.: 6.3892  
   GSM674372         GSM674373         GSM674374         GSM674375         GSM674376         GSM674377         GSM674378      
 Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477  
 1st Qu.: 1.8598   1st Qu.: 1.8518   1st Qu.: 1.8523   1st Qu.: 1.8589   1st Qu.: 1.8586   1st Qu.: 1.8578   1st Qu.: 1.8479  
 Median : 3.1118   Median : 3.1015   Median : 3.1006   Median : 3.0980   Median : 3.1038   Median : 3.1017   Median : 3.1017  
 Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540  
 3rd Qu.: 6.3893   3rd Qu.: 6.3890   3rd Qu.: 6.3894   3rd Qu.: 6.3886   3rd Qu.: 6.3884   3rd Qu.: 6.3895   3rd Qu.: 6.3895  
   GSM674379         GSM674380         GSM674381         GSM674382         GSM674383         GSM674384         GSM674385      
 Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477  
 1st Qu.: 1.8578   1st Qu.: 1.8595   1st Qu.: 1.8497   1st Qu.: 1.8546   1st Qu.: 1.8561   1st Qu.: 1.8506   1st Qu.: 1.8557  
 Median : 3.0977   Median : 3.0997   Median : 3.1013   Median : 3.1061   Median : 3.1017   Median : 3.1025   Median : 3.1071  
 Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540  
 3rd Qu.: 6.3894   3rd Qu.: 6.3881   3rd Qu.: 6.3884   3rd Qu.: 6.3890   3rd Qu.: 6.3895   3rd Qu.: 6.3893   3rd Qu.: 6.3894  
   GSM674386         GSM674387         GSM674388         GSM674389         GSM674390         GSM674391         GSM674392      
 Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5757   Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477  
 1st Qu.: 1.8557   1st Qu.: 1.8479   1st Qu.: 1.8541   1st Qu.: 1.8595   1st Qu.: 1.8512   1st Qu.: 1.8519   1st Qu.: 1.8545  
 Median : 3.0951   Median : 3.1034   Median : 3.1062   Median : 3.0917   Median : 3.1006   Median : 3.0997   Median : 3.1015  
 Mean   : 4.2541   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540  
 3rd Qu.: 6.3879   3rd Qu.: 6.3894   3rd Qu.: 6.3893   3rd Qu.: 6.3888   3rd Qu.: 6.3892   3rd Qu.: 6.3886   3rd Qu.: 6.3890  
   GSM674393         GSM674394         GSM674395         GSM674396         GSM674397         GSM674398         GSM674399      
 Min.   : 0.5477   Min.   : 0.5757   Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477  
 1st Qu.: 1.8554   1st Qu.: 1.8505   1st Qu.: 1.8467   1st Qu.: 1.8517   1st Qu.: 1.8534   1st Qu.: 1.8513   1st Qu.: 1.8620  
 Median : 3.1066   Median : 3.0967   Median : 3.1019   Median : 3.0929   Median : 3.1057   Median : 3.1038   Median : 3.1092  
 Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540  
 3rd Qu.: 6.3895   3rd Qu.: 6.3895   3rd Qu.: 6.3881   3rd Qu.: 6.3895   3rd Qu.: 6.3890   3rd Qu.: 6.3895   3rd Qu.: 6.3900  
   GSM674400         GSM674401         GSM674402         GSM674403         GSM674404         GSM674405         GSM674406      
 Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477   Min.   : 0.5477  
 1st Qu.: 1.8481   1st Qu.: 1.8612   1st Qu.: 1.8486   1st Qu.: 1.8523   1st Qu.: 1.8530   1st Qu.: 1.8601   1st Qu.: 1.8594  
 Median : 3.0915   Median : 3.0999   Median : 3.1074   Median : 3.1106   Median : 3.1046   Median : 3.1061   Median : 3.0948  
 Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540   Mean   : 4.2540  
 3rd Qu.: 6.3890   3rd Qu.: 6.3871   3rd Qu.: 6.3890   3rd Qu.: 6.3898   3rd Qu.: 6.3894   3rd Qu.: 6.3881   3rd Qu.: 6.3884  
   GSM674407      
 Min.   : 0.5477  
 1st Qu.: 1.8518  
 Median : 3.1019  
 Mean   : 4.2540  
 3rd Qu.: 6.3895  
 [ reached getOption("max.print") -- omitted 1 row ]

If this output we clearly see that the values go beyond 16, so we will need to perform a log2 transformation. A boxplot can also be generated to see if the data have been normalised. If so, the distributions of each sample should be highly similar.

exprs(gsePS) <- log2(exprs(gsePS))
boxplot(exprs(gsePS),outline=FALSE)


exprs(gseAS) <- log2(exprs(gseAS))
boxplot(exprs(gseAS),outline=FALSE)

Inspect the clinical variables. Data submitted to GEO contain sample labels assigned by the experimenters, and some information about the processing protocol. All these data can be extracted by the pData function.

For your own data, you will have to decide which columns will be useful in the analysis. This will include the column giving the main comparison(s) of interest and any potential confounding factors. In this particular data-set it looks like source_name_ch1 and characteristics_ch1.1.

We can use the select function from dplyr to display just these columns of interest. At this stage it will also be useful to rename the columns to something more convenient using the rename function.

library (dplyr)

Attaching package: ‘dplyr’

The following object is masked from ‘package:Biobase’:

    combine

The following objects are masked from ‘package:BiocGenerics’:

    combine, intersect, setdiff, union

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union
sampleInfoPS <- pData(gsePS)
print(sampleInfoPS)

sampleInfoAS <- pData(gseAS)
print(sampleInfoAS)
## source_name_ch1 and characteristics_ch1.1 seem to contain factors we might need for the analysis. Let's pick just those columns
sampleInfoPS <- select(sampleInfoPS, source_name_ch1, characteristics_ch1.1)
sampleInfoAS <- select(sampleInfoAS, source_name_ch1, characteristics_ch1.1)

## Optionally, rename to more convenient column names
sampleInfoPS <- rename(sampleInfoPS,group = source_name_ch1, patient=characteristics_ch1.1)
sampleInfoAS <- rename(sampleInfoAS,group = source_name_ch1, patient=characteristics_ch1.1)
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